EG VCBM 2019
Eurographics Workshop on Visual Computing for Biology and Medicine – Full and Short Paper Proceedings –
Brno, Czech Republic September 4 – 6, 2019
Programme Chairs (Full Papers)
Barbora Kozlíková (Masaryk University, Czech Republic) Lars Linsen (University of Münster, Germany)
Pere-Pau Vázquez (Universitat Politècnica de Catalunya, Spain)
Programme Chairs (Short Papers) Kai Lawonn (University of Koblenz, Germany)
Renata Georgia Raidou (TU Wien, Austria)
Programme Chairs (Posters) Jan Byška (University of Bergen, Norway)
Gabriel Mistelbauer (University of Magdeburg, Germany)
General Chairs
Barbora Kozlíková (Masaryk University, Czech Republic) Renata Georgia Raidou (TU Wien, Austria)
Proceedings Production Editor
Dieter Fellner (TU Darmstadt & Fraunhofer IGD, Germany)
DOI: 10.2312/vcbm.20192019 https://www.eg.org https://diglib.eg.org
Dieter W. Fellner, Werner Hansmann, Werner Purgathofer, François Sillion Series Editors
This work is subject to copyright.
All rights reserved, whether the whole or part of the material is concerned, specifically those of translation, reprinting, re-use of illustrations, broadcasting, reproduction by photocopying machines or similar means, and storage in data banks.
Copyright c2019 by the Eurographics Association Postfach 2926, 38629 Goslar, Germany
Published by the Eurographics Association –Postfach 2926, 38629 Goslar, Germany–
in cooperation with
Institute of Computer Graphics & Knowledge Visualization at Graz University of Technology and
Fraunhofer IGD (Fraunhofer Institute for Computer Graphics Research), Darmstadt ISBN 978-3-03868-081-9
ISSN 2070-5786 (online)
The electronic version of the proceedings is available from the Eurographics Digital Library at https://diglib.eg.org
Table of Contents
Table of Contents . . . iii
Organisation and Sponsors . . . vi
International Program Committee . . . vii
Author Index . . . viii
Keynote and Capstone . . . x
Visual Computing for MRI-based Data SpectraMosaic: An Exploratory Tool for the Interactive Visual Analysis of Magnetic Resonance Spectroscopy Data . . . 1
Laura Garrison, Jakub Vašíˇcek, Renate Grüner, Noeska N. Smit, and Stefan Bruckner Multiparametric Magnetic Resonance Image Synthesis using Generative Adversarial Networks . . . 11
Christoph Haarburger, Nicolas Horst, Daniel Truhn, Mirjam Broeckmann, Simone Schrading, Christiane Kuhl, and Dorit Merhof Colonic Content Assessment from MRI Imaging Using a Semi-automatic Approach . . . 17
Victor Ceballos, Eva Monclús, Pere-Pau Vázquez, Álvaro Bendezú, Marianela Mego, Xavier Merino, Fernando Azpiroz, and Isabel Navazo A Web-based Application for the Visual Exploration of Colon Morphology Data . . . 27
Jan Males, Eva Monclús, Jose Díaz, and Pere-Pau Vázquez Interactive Formation of Statistical Hypotheses in Diffusion Tensor Imaging . . . 33
Amin Abbasloo, Vitalis Wiens, Tobias Schmidt-Wilcke, Pia Sundgren, Reinhard Klein, and Thomas Schultz Semantic Segmentation of Brain Tumors in MRI Data Without any Labels . . . 45
Leon Weninger, Imke Krauhausen, and Dorit Merhof Visual Analytics in Medicine and Biology Feasibility Study For Automatic Bird Tracking and Visualization from Time-Dependent Marine Radar Imagery 51 Florian Ganglberger and Katja Bühler A Visual Environment for Hypothesis Formation and Reasoning in Studies with fMRI and Multivariate Clinical Data . . . 57
Daniel Jönsson, Albin Bergström, Camilla Forsell, Rozalyn Simon, Maria Engström, Anders Ynnerman, and Ingrid Hotz Pelvis Runner: Visualizing Pelvic Organ Variability in a Cohort of Radiotherapy Patients . . . 69
Nicolas Grossmann, Oscar Casares-Magaz, Ludvig Paul Muren, Vitali Moiseenko, John P. Einck, Eduard Gröller, and Renata Georgia Raidou preha: Establishing Precision Rehabilitation with Visual Analytics . . . 79 Georg Bernold, Kresimir Matkovic, Eduard Gröller, and Renata Georgia Raidou
Table of Contents
A Visual Analytics Approach for Patient Stratification and Biomarker Discovery . . . 91 Shiva Alemzadeh, Florian Kromp, Bernhard Preim, Sabine Taschner-Mandl, and Katja Bühler
MedUse: A Visual Analysis Tool for Medication Use Data in the ABCD Study . . . 97 Hauke Bartsch, Laura Garrison, Stefan Bruckner, Ariel Wang, Susan F. Tapert, and Renate Grüner
Molecular Visualization (I)
Interactive Exploded Views for Molecular Structures . . . 103 Maximilian Sbardellati, Haichao Miao, Hsiang-Yun Wu, Eduard Gröller, Ivan Barisic, and Ivan Viola
DockVis: Visual Analysis of Molecular Docking Data . . . 113 Katarína Furmanová, Barbora Kozlíková, Vojtˇech Vonásek, and Jan Byška
Digital Pathology, Surgery, and Anatomical Education
Layer-Aware iOCT Volume Rendering for Retinal Surgery . . . 123 Jakob Weiss, Ulrich Eck, Muhamad Ali Nasseri, Mathias Maier, Abouzar Eslami, and Nassir Navab
Visual Analytics in Digital Pathology: Challenges and Opportunities . . . 129 Alberto Corvò, Michel A. Westenberg, Reinhold Wimberger-Friedl, Stephan Fromme, Michel M. R. Peeters, Marc A. van Driel, and Jarke J.van Wijk
Animation, Tracking, and Simulations
Medical Animations: A Survey and a Research Agenda . . . 145 Bernhard Preim and Monique Meuschke
Using Position-Based Dynamics for Simulating the Mitral Valve in a Decision Support System . . . 165 Lars Walczak, Joachim Georgii, Lennart Tautz, Mathias Neugebauer, Isaac Wamala, Simon Sündermann,
Volkmar Falk, and Anja Hennemuth
InkVis: A High-Particle-Count Approach for Visualization of Phase-Contrast Magnetic Resonance Imaging Data . . . 177 Niels H. L. C. de Hoon, Kai Lawonn, Andrei C. Jalba, Elmar Eisemann, and Anna Vilanova
Robustness Evaluation of CFD Simulations to Mesh Deformation . . . 189 Alexander Scheid-Rehder, Kai Lawonn, and Monique Meuschke
The Vitruvian Baby: Interactive Reformation of Fetal Ultrasound Data to a T-Position . . . 201 Eric Mörth, Renata Georgia Raidou, Ivan Viola, and Noeska N. Smit
HIFUpm: a Visual Environment to Plan and Monitor High Intensity Focused Ultrasound Treatments . . . 207 Daniela Modena, Davide Bassano, Aaldert Elevelt, Marco Baragona, Peter A. J. Hilbers, and Michel A.
Westenberg
Table of Contents
Molecular Visualization (II)
Hybrid Visualization of Protein-Lipid and Protein-Protein Interaction . . . 213 Naif Alharbi, Michael Krone, Matthieu Chavent, and Robert S. Laramee
Molecular Sombreros: Abstract Visualization of Binding Sites within Proteins . . . 225 Karsten Schatz, Michael Krone, Tabea L. Bauer, Valerio Ferrario, Jürgen Pleiss, and Thomas Ertl
Interactive CPU-based Ray Tracing of Solvent Excluded Surfaces . . . 239 Tobias Rau, Sebastian Zahn, Michael Krone, Guido Reina, and Thomas Ertl
Blood Flow and Vascular Visualization
Evolutionary Pathlines for Blood Flow Exploration in Cerebral Aneurysms . . . 253 Benjamin Behrendt, Wito Engelke, Philipp Berg, Oliver Beuing, Bernhard Preim, Ingrid Hotz, and
Sylvia Saalfeld
Distance Field Visualization and 2D Abstraction of Vessel Tree Structures with on-the-fly
Parameterization . . . 265 Nils Lichtenberg, Bastian Krayer, Christian Hansen, Stefan Müller, and Kai Lawonn
Organisation and Sponsors
International Program Committee Benjamin Berkels (RWTH Aachen, Germany)
Johanna Beyer (Harvard University, USA) Stefan Bruckner (University of Bergen, Norway) Katja Bühler (VRVis Vienna, Austria)
Eduard Gröller (TU Wien, Austria)
Markus Hadwiger (KAUST, Saudi-Arabia)
Christian Hansen (University of Magdeburg, Germany) Hans-Christian Hege (Zuse Institute Berlin, Germany) Anja Hennemuth (Charité Berlin, Germany)
Thomas Höllt (TU Delft, The Netherlands) Ingrid Hotz (Linköping University, Sweden)
Barbora Kozlíková (Masaryk Unversity, Czech Republic) Michael Krone (University of Tübingen, Germany) David Laidlaw (Brown University, USA)
Kai Lawonn (University of Koblenz, Germany) Lars Linsen (University of Münster, Germany)
Andreas Maier (University of Erlangen-Nürnberg, Germany) Klaus Maier-Hein (DKFZ Heidelberg, Germany)
G. Elizabeta Marai (University of Illinois, Chicago) David Mayerich (University of Houston, USA) Björn Menze (TU München, Germany) Dorit Merhof (RWTH Aachen, Germany)
Gabriel Mistelbauer (University of Magdeburg, Germany) Vijay Natarajan (Indian Institute of Science Bangalore, India) Steffen Oeltze-Jafra (University of Magdeburg, Germany) Bernhard Preim (University of Magdeburg, Germany) Renata Georgia Raidou (TU Wien, Austria)
Guido Reina (University of Stuttgart, Germany) Timo Ropinski (University of Ulm, Germany) Thomas Schultz (University of Bonn, Germany) Noeska Natasja Smit (University of Bergen, Norway) Pere-Pau Vázquez (U.P.C. Barcelona, Spain)
Franck Vidal (Bangor University, UK) Anna Vilanova (TU Delft, The Netherlands)
Michel Westenberg (TU Eindhoven, The Netherlands) Stefan Zachow (Zuse Institute Berlin, Germany)
Author Index
Abbasloo, Amin . . . 33
Alemzadeh, Shiva . . . 91
Alharbi, Naif . . . 213
Azpiroz, Fernando . . . 17
Baragona, Marco . . . 207
Barisic, Ivan . . . 103
Bartsch, Hauke . . . 97
Bassano, Davide . . . 207
Bauer, Tabea L. . . 225
Behrendt, Benjamin . . . 253
Bendezú, Álvaro . . . 17
Berg, Philipp . . . 253
Bergström, Albin . . . 57
Bernold, Georg . . . 79
Beuing, Oliver . . . 253
Broeckmann, Mirjam . . . 11
Bruckner, Stefan . . . 1, 97 Bühler, Katja . . . 51, 91 Byška, Jan . . . 113
Casares-Magaz, Oscar . . . 69
Ceballos, Victor . . . 17
Chavent, Matthieu . . . 213
Corvò, Alberto . . . 129
Díaz, Jose . . . 27
Driel, Marc A. van . . . 129
Eck, Ulrich . . . 123
Einck, John P. . . 69
Eisemann, Elmar . . . 177
Elevelt, Aaldert . . . 207
Engelke, Wito . . . 253
Engström, Maria . . . 57
Ertl, Thomas . . . 225, 239 Eslami, Abouzar . . . 123
Falk, Volkmar . . . 165
Ferrario, Valerio . . . 225
Forsell, Camilla . . . 57
Fromme, Stephan . . . 129
Furmanová, Katarína . . . 113
Ganglberger, Florian . . . 51
Garrison, Laura . . . 1, 97 Georgii, Joachim . . . 165
Gröller, Eduard . . . 69, 79, 103 Grossmann, Nicolas . . . 69
Grüner, Renate . . . 1, 97 Haarburger, Christoph . . . 11
Hansen, Christian . . . 265
Hennemuth, Anja . . . 165
Hilbers, Peter A. J. . . 207
Hoon, Niels H. L. C. de . . . 177
Horst, Nicolas . . . 11
Hotz, Ingrid . . . 57, 253 Jalba, Andrei C. . . 177
Jönsson, Daniel . . . 57
Klein, Reinhard . . . 33
Kozlíková, Barbora . . . 113
Krauhausen, Imke . . . 45
Krayer, Bastian . . . 265
Kromp, Florian . . . 91
Krone, Michael . . . 213, 225, 239 Kuhl, Christiane . . . 11
Laramee, Robert S. . . 213
Lawonn, Kai . . . 177, 189, 265 Lichtenberg, Nils . . . 265
Maier, Mathias . . . 123
Males, Jan . . . 27
Matkovic, Kresimir . . . 79
Mego, Marianela . . . 17
Merhof, Dorit . . . 11, 45 Merino, Xavier . . . 17
Meuschke, Monique . . . 145, 189 Miao, Haichao . . . 103
Modena, Daniela . . . 207
Moiseenko, Vitali . . . 69
Monclús, Eva . . . 17, 27 Mörth, Eric . . . 201
Müller, Stefan . . . 265
Muren, Ludvig Paul . . . 69
Nasseri, Muhamad Ali . . . 123
Navab, Nassir . . . 123
Navazo, Isabel . . . 17
Neugebauer, Mathias . . . 165
Peeters, Michel M. R. . . 129
Pleiss, Jürgen . . . 225
Preim, Bernhard . . . 91, 145, 253 Raidou, Renata Georgia . . . 69, 79, 201 Rau, Tobias . . . 239
Reina, Guido . . . 239
Saalfeld, Sylvia . . . 253
Sbardellati, Maximilian . . . 103
Schatz, Karsten . . . 225
Author Index
Scheid-Rehder, Alexander . . . 189
Schmidt-Wilcke, Tobias . . . 33
Schrading, Simone . . . 11
Schultz, Thomas . . . 33
Simon, Rozalyn . . . 57
Smit, Noeska N. . . 1, 201 Sündermann, Simon . . . 165
Sundgren, Pia . . . 33
Tapert, Susan F. . . 97
Taschner-Mandl, Sabine . . . 91
Tautz, Lennart . . . 165
Truhn, Daniel . . . 11
Vašíˇcek, Jakub . . . 1
Vázquez, Pere-Pau . . . 17, 27 Vilanova, Anna . . . 177
Viola, Ivan . . . 103, 201 Vonásek, Vojtˇech . . . 113
Walczak, Lars . . . 165
Wamala, Isaac . . . 165
Wang, Ariel . . . 97
Weiss, Jakob . . . 123
Weninger, Leon . . . 45
Westenberg, Michel A. . . 129, 207 Wiens, Vitalis . . . 33
Wijk, Jarke J. van . . . 129
Wimberger-Friedl, Reinhold . . . 129
Wu, Hsiang-Yun . . . 103
Ynnerman, Anders . . . 57
Zahn, Sebastian . . . 239
Keynote Advanced Visualization for Computational Protein Design
Jiˇrí Damborský
Abstract
Enzymes are natural catalysts of living organisms, which find broad use in biotechnological processes, biopharmaceuticals and biomaterials. Modern enzymes have evolved for the catalysis in an aqueous en- vironment under mild conditions and therefore often do not meet requirements of practical applications.
Two major streams in protein engineering are the rational design and directed evolution. The Nobel Prize in Chemistry 2013 was awarded to Martin Karplus, Michael Levitt and Arieh Warshel for the develop- ment of multiscale models for complex chemical systems, used extensively in rational protein design.
Nobel Prize in Chemistry 2018 has been awarded to Frances Arnold for the development of directed evo- lution of enzymes. Both approaches can be combined in a single workflow employing rational design for the selection of “hot spots” and directed evolution for their combinatorial mutagenesis.
Biographical Note
Prof. Mgr. Jiˇrí Damborský, Dr. is the Josef Loschmidt Chair Professor of Chemistry and Professor of Biochemistry at the Faculty of Science at Masaryk University in Brno, Czech Republic and a group leader at the International Centre for Clinical Research. Research of his group focuses on protein engineering.
His group develops new concepts and software tools for protein engineering (CAVER, CAVERDOCK, HOTSPOT WIZARD, PREDICTSNP, FIREPROT, CALFITTER), and uses them for the computational design of enzymes. He has published 200 original articles, 18 book chapters and filed 7 international patents. He is a co-founder of the first biotechnology spin-off from Masaryk University Enantis Ltd.
Among the awards and distinctions he has received is the award EMBO/HHMI Scientist of the European Molecular Biology Organisation and the Howard Hughes Medical Institute.
Capstone
Visual Computing for Advanced Image-guided Interventions and Image Reconstruction
Wolfgang Wein
Abstract
Both ever-increasing computing power as well as data availability benefit the medical imaging domain, however, they have to be carefully paired with methodological advancements. For one, more powerful real-time image processing enables image-guided interventions in previously too difficult scenarios. Also, 3D medical image reconstruction from raw measurement data can be done with more and more realistic modeling of the underlying imaging physics, as well as sophisticated organ- and application-specific prior models. Such reconstruction methods are then increasingly tailored for specific clinical requirements, and directly involve the extraction of content rather than display of images only. This talk first highlights some emerging applications of ultrasound image guidance and their enabling technologies. It then connects with advanced physics-based reconstruction from both ultrasonic and X-Ray imaging data, and the emerging role of deep learning in all of this. The presentation concludes by listing major trends and challenges ahead, as well as discussing business aspects of innovation in the medical device sector.
Biographical Note
Dr. Wolfgang Wein has worked in medical image computing research for the last 15 years, conducting numerous projects from early feasibility to product implementation. He received his doctoral degree in 2007 from Prof. Navab at the group for Computer Aided Medical Procedures (CAMP) at TU Munich, Germany. From 2006-2010 he worked as a research scientist at Siemens Corporate Research in Princeton, NJ USA, on various interventional navigation and medical imaging projects. In 2012, he founded the R&D lab ImFusion in Munich, which aids medical device companies around the world to create innovation. He also has a teaching assignment at TU Munich.
